Check your memory usage in Task Manager (ctrl-alt-del, select Task Manager). My first guess is some program you've installed on both copies of Windows has a memory leak. When you reboot, it takes up very little memory so everything is fine. As the hours tick by, it consumes more memory, forcing Windows to start moving memory pages to the pagefile on the disk. Pagefile accesses then slow down other drive access.
Or if you're like most people and keep a browser running with a bunch of tabs open all the time, those can end up using a large amount of RAM. Which again can result in Windows having to use the pagefile.